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Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology Part 2: DNA to protein Coming attractions! Significance.

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Presentation on theme: "Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology Part 2: DNA to protein Coming attractions! Significance."— Presentation transcript:

1 Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology Part 2: DNA to protein Coming attractions! Significance Palindromes (SQ4) Why introns? (SQ8) Types of mutation (SQ12)

2 Study Question 8 Why do introns exist? I do not understand why introns would even exist. I dont understand why the information for a single element would be spread out. Well, they do seem pretty mysterious. I’ll quickly review what introns and exons are and then propose an explanation as to why they might serve a useful purpose.

3 Study Question 8 Why do introns exist? DNA Primary transcript (hnRNA) Transcription Transcription is a key step in the expression of genes, i.e. the chain of events that convert information on DNA into cell behavior. The end product of transcription is a molecule of RNA corresponding to a small fraction of the DNA.

4 Study Question 8 Why do introns exist? AAAAAA...AAA DNA Primary transcript (hnRNA) Me G capPoly-A tail Transcription In eukaryotes, the primary transcript (i.e. the direct RNA product of transcription) is processed before it is used in translation. One modification is a special guanosine placed at the 5’ end of the message. Another is a string of adenosines placed at the 3’ end of the message.

5 Study Question 8 Why do introns exist? AAAAAA...AAA DNA Primary transcript (hnRNA) Me G capPoly-A tail Transcription They function in the stability of the message and in helping ribosomes bind to the RNA’s 5’ end. However, poly-A tails are much less important in bacteria and their viruses, and caps are (to my knowledge) absent. Since we will be focusing on bacterial viruses, these structures needn’t concern us now.

6 Study Question 8 Why do introns exist? AAAAAA...AAA DNA Primary transcript (hnRNA) Me G capPoly-A tail Transcription Transcripts are subject to a third modification. If you looked at the sequence of a transcript, you would not find anything in one region to distinguish it from another. However protein-nucleic acid complexes in the nucleus of eukaryotic cells recognize certain sites ( ) in the message.

7 Study Question 8 Why do introns exist? AAAAAA...AAA Splicing Primary transcript (hnRNA) Processed transcript (mRNA) Me G capPoly-A tail Intron Exon These complexes cause some of the RNA to be cut out, a process called splicing. RNA that’s cut out is called an intron. RNA that’s left in is called an exon.

8 Study Question 8 Why do introns exist? AAAAAA...AAA Splicing Primary transcript (hnRNA) Processed transcript (mRNA) Me G capPoly-A tail Intron Exon It is the mature, processed transcript that enters the cytoplasm and is translated by ribosomes.

9 Study Question 8 Why do introns exist? AAAAAA...AAA Splicing Primary transcript (hnRNA) Processed transcript (mRNA) Me G capPoly-A tail Intron Exon Where are introns when translation takes place? …what role [does] an intron plays in translation?

10 Study Question 8 Why do introns exist? AAAAAA...AAA Splicing Primary transcript (hnRNA) Processed transcript (mRNA) Me G capPoly-A tail Intron Exon You could answer this question the same way you discovered what is the beginning of a gene. What would you need to do this? …could you explain… how a cell's apparatus distinguishes exon from intron?

11 Study Question 8 Why do introns exist? That explains what introns are, but not why they exist. They’re not necessary… bacteria live perfectly well even though introns are very rare in bacteria and their viruses. In eukaryotes, however, they are very common. Why? How do introns contribute to differences between eukaryotes and prokaryotes?

12 Study Question 8 Why do introns exist? Huge differences amongst bacterial DNA sequences Small differences in morphology Bacterial sequences change rapidly in evolutionary time, but major changes in morphology are rare.

13 Study Question 8 Why do introns exist? Small differences amongst vertebrate DNA sequences Large differences in morphology http://uncyclopedia.wikia.com/wiki/User:Skinfan13/Upsil on_Sigma_Sigma/Collaboration/May2010collab In contrast, eukaryotes can look very different, even though the sequences of their genes are similar. The gene sequences of mammals are generally very similar to each other. They differ in the adjacent regulatory sequences that control gene expression.

14 Study Question 8 Why do introns exist? Hormone-responsive protein kinase hormone responsiveness protein kinase Here’s an example of how introns can contribute to a drastic change in phenotype without a drastic change in sequence. Suppose that there is a gene that encodes an enzyme that responds to a hormone. The first part of the gene encodes the part of the protein that recognizes the hormone, and the rest encodes the enzyme.

15 Study Question 8 Why do introns exist? Hormone-responsive protein kinase hormone responsiveness DNA binding protein kinase DNA-binding protein Now suppose that there is a second gene, lying very far away on the chromosome (or even on a different chromosome). This gene encodes a DNA-binding protein..

16 Study Question 8 Why do introns exist? hormone responsiveness DNA binding protein kinase Since DNA frequently recombines, breaking and joining with other regions of the chromosome, the two genes may by accident find themselves close to each other. Maybe they’re close enough so that a single RNA is transcribed

17 Study Question 8 Why do introns exist? hormone responsiveness DNA binding protein kinase Now the splice sites are close enough to produce, after splicing, an mRNA that would encode a novel protein. In bacteria, the DNA recombination would have to be exact. In eukaryotes, somewhere in the vicinity will do. Hormone-responsive DNA-binding protein

18 Study Question 8 Why do introns exist? hormone responsiveness DNA binding protein kinase Introns therefore can greatly accelerate the rate of evolution of proteins of novel functions. For more on exon shuffling, see Keren H et al (2010). Nature Rev Genet 11:345-355. Hormone-responsive DNA-binding protein

19 Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology Part 2: DNA to protein Coming attractions! Significance Palindromes (SQ4) Why introns? (SQ8) Types of mutation (SQ12)

20 Study Question 12 Single mutation from AGA If this question is confusing, take it apart bit by bit.

21 Study Question 12 Single mutation from AGA …the AGA codon… That, at least, might be clear. Write it down! AGA arginine

22 Study Question 12 Single mutation from AGA …a single basepair mutation… What could that mean? AGA arginine

23 Study Question 12 Single mutation from AGA Basepair? Of course DNA is double stranded, so a codon in DNA is paired with complementary nucleotides. What would be the basepairs of the AGA codon? AGA arginine

24 Study Question 12 Single mutation from AGA Wait, that’s not enough. With double stranded DNA, you need to show the direction of each strand. Where should you put 5’ and where 3’? AGA arginine TCT

25 Study Question 12 Single mutation from AGA Yes. Codons (like any other DNA or RNA sequence) are read 5’ to 3’. What kind of single basepair mutations are possible? What’s an example of a single basepair? AGA arginine TCT 5’- 3’- -3’ -5’

26 Study Question 12 Single mutation from AGA That’s one basepair. What are some possible changes? AGA arginine TCT 5’- 3’- -3’ -5’

27 Study Question 12 Single mutation from AGA OK, that’s one possible change. How many total possible changes are there? Note I said “possible”. A G/A basepair is not possible. AGA arginine TCT 5’- 3’- -3’ -5’ GGA arginine CCT 5’- 3’- -3’ -5’

28 Study Question 12 Single mutation from AGA I’m not going to write basepairs anymore – you can always imagine them. Nor am I going to write 5’ and 3’. Remember, unless specified, left-to-right is always 5’ to 3’. AGA arginine

29 Study Question 12 Single mutation from AGA Moving on, what could “encoding arginine” mean? I’ll pause so you could look up what arginine is. (Google is your friend) AGA arginine

30 Study Question 12 Single mutation from AGA …an amino acid. Codons encode amino acids. AGA arginine

31 Study Question 12 Single mutation from AGA So putting it all together…. …what does the first part of the question mean? AGA arginine

32 Study Question 12 Single mutation from AGA Single basepair mutations in AGA change the codon. Changing the codon may change the amino acid that’s encoded. Which single basepair changes produce which changes in encoded amino acids? AGA arginine

33 Study Question 12 Single mutation from AGA What might these terms mean? They’re likely to refer to the result of the changes described in the first part of the question, changes in codons and perhaps the amino acids they encode. Start with two we’ve discussed: hydrophobic and hydrophilic AGA arginine

34 Study Question 12 Single mutation from AGA Look at Figure 2 from the notes on Proteins. Notice that the amino acids are arranged in a very similar manner to the generic amino acid shown in Figure 1. There is a constant part that all amino acids have, and there is a variable part, labeled R. Proteins, Figure 2 Proteins, Figure 1 Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub

35 Study Question 12 Single mutation from AGA I’ve represented the constant part as shadowed. What distinguishes one amino acid from the others is what’s left. Consider the amino acids with hydrophobic R groups. What generality can you draw from their chemical constituents? Proteins, Figure 2 Proteins, Figure 1 Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub

36 Study Question 12 Single mutation from AGA Look at them! Except for methionine, they consist solely of carbons and hydrogens. They’re hydrocarbons, like oil. What about the negatively charged R groups? Proteins, Figure 2 Proteins, Figure 1 Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub

37 Study Question 12 Single mutation from AGA Proteins, Figure 2 Proteins, Figure 1 Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub All the negatively charged R groups have free carboxylate moieties ( ), with negative charges. Positively-charged R groups? -C-O - O

38 Study Question 12 Single mutation from AGA Proteins, Figure 2 Proteins, Figure 1 Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub All positively charged nitrogen atoms in some form. Finally, the hydrophilic, uncharged R groups?

39 Study Question 12 Single mutation from AGA Proteins, Figure 2 Proteins, Figure 1 Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub …a mixed bag, but all of them have uncharged polar groups, for example -OH. Of course, they are different in other ways: some are large, some small, some have aromatic rings, others not. Each has a different flavor.

40 Study Question 12 Single mutation from AGA Now back to the question. AGA encodes arginine. Mutations can change the codon. That might change the encoded amino acid. That might change the type of amino acid. We have something that describes the types of amino acids (left). We need a table that connects amino acids to their codons. AGA arginine GGA ???

41 Study Question 12 Single mutation from AGA Here's such a table. You can find dozens of these on the web, or use the genetic table found on the Resources & Links section. First of all, does AGA indeed encode arginine? Learn how to use this table.

42 Study Question 12 Single mutation from AGA How many ways can AGA be changed by a single nucleotide? Answer this by counting, and then figure out how you could calculate the number. How many ways could a 10-letter sequence be changed by a single nucleotide?

43 Study Question 12 Single mutation from AGA …Back to AGA. Categorize each change to AGA, using the labels given in the question. How does the encoded amino acid change in each case?

44 If "conservative" is "close enough", how close is that? Study Question 12 Single mutation from AGA (Frequently asked questions) A conservative amino acid substitution is one that should not affect the function of the protein. However, this is often not easy to predict. In one context, leucine and isoleucine might be interchangeable, while in another, substituting isoleucine for leucine could lead to an inactive protein. That isn't a satisfying answer, but it does reflect our current state of knowledge.

45 If "conservative" is "close enough", how close is that? Study Question 12 Single mutation from AGA (Frequently asked questions) If you do, you will. If the time ever comes when you find yourself constantly going back to a list of amino acids and their properties, you will memorize them without trying. Until then, the list is always available. Do we have to learn the 20 amino acids?

46 If "conservative" is "close enough", how close is that? Study Question 12 Single mutation from AGA (Frequently asked questions) Well now, funny you should ask! Do we have to learn the 20 amino acids? Will we be able to decipher the genetic code of an alien being?

47 If you go to the Intro to Molecular Biology topic page, you will find a link to an investigation called Alien Genetic Code.

48 Alien Genetic Code (Coming Attractions!) C C CC C CC C C C C C Pro-Pro-Pro-Pro… Terrestrial Genetic Code Terrestrial ribosomes There you will be given the means to perform virtual experiments. Using terrestrial cell extracts and the RNA CCCCC…, these experiments would produce poly-proline, according to our genetic code.

49 C C CC C CC C C C C C Alien Genetic Code Alien ribosomes ? ? ? ` Alien Genetic Code (Coming Attractions!) But using alien cell extracts... who knows? You can know.


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